Uveal melanoma (UM) is described in the source as the most common primary eye cancer and is associated with a high mortality burden. The authors report an overall mortality rate of 80% and note that only 1–3% of patients have detectable UM at the time of metastasis. UM growth is characterized as punctuated early in disease evolution.
Given prior reports that the antibiotic doxycycline can inhibit metabolic pathways exploited by cancer cells and reduce cancer cell growth in liver cancer models, the authors tested whether doxycycline might similarly modulate UM‑relevant biology in a human ocular organoid model.
To model UM‑associated changes, the investigators used a human stem cell line engineered with a tetracycline‑inducible system to knock down BAP1, a gene implicated in UM biology. Cells from this line were differentiated into whole‑eye organoids termed SEAM (self‑formed ectodermal autonomous multi‑zone of ocular cells), which contain multiple ocular cell types and permit in vitro study of ocular lineage behavior.
The source reports that the BAP1 knockdown produced a phenotype described as a UM model (BAP1 KD, UM phenotype) within the SEAM organoids, thereby enabling downstream molecular and functional analyses relevant to uveal melanoma.
Within the SEAM colonies derived from the BAP1 KD condition, the authors observed an enhanced proliferation specifically in neural crest cell populations. To identify and characterize these neural crest cells more precisely, the study applied transcriptomic approaches (see next section) and then selected genes of interest from neural crest clusters for further validation.
The authors performed single‑cell RNA sequencing (scRNA‑seq) and analyzed the data using the Seurat R toolkit to define clusters and identify genes expressed in neural crest populations. This analysis was used to pinpoint genes within neural crest clusters that could be relevant to UM proliferation, angiogenesis, and cellular metabolism, including oxidative phosphorylation pathways.
The source indicates that the scRNA‑seq results supported the identification of molecular signatures in the BAP1 KD organoids that align with UM‑relevant biology, though specific gene names, cluster sizes, sequencing depth, or statistical metrics were not reported in the source summary.
To confirm the scRNA‑seq findings, the investigators assessed selected genes with notable functions using immunofluorescence and RT‑qPCR. These orthogonal assays were applied to genes differentially expressed in the neural crest cluster and implicated in proliferation, angiogenesis, and oxidative phosphorylation.
According to the source, results from immunofluorescence and RT‑qPCR corroborated the in silico findings and demonstrated that the BAP1 KD organoid model recapitulated UM‑relevant gene and protein expression patterns. The source does not provide the exact markers or quantitative results in the summary.
After establishing that the BAP1 KD SEAM organoid reproduced UM‑associated marker expression, the authors treated the BAP1 KD (UM phenotype) and control organoids with doxycycline to evaluate its effects on UM‑relevant endpoints.
The source reports that doxycycline treatment significantly inhibited metrics interpreted as UM growth, angiogenesis, and oxidative phosphorylation in the BAP1 KD organoids to a greater degree than in control organoids. The authors suggest this preferential effect may reflect doxycycline targeting regions or cell populations with higher mitochondrial activity.
Specific experimental parameters for doxycycline dosing, treatment duration, quantitative effect sizes, and statistical analyses are not detailed in the provided summary.
Based on the organoid data, the authors propose that doxycycline has therapeutic potential for uveal melanoma, particularly in the context of BAP1 repression. The study presents a preclinical in vitro model—human SEAM ocular organoids with inducible BAP1 knockdown—that reproduces UM‑relevant molecular signatures and allows evaluation of metabolic and growth effects of doxycycline.
Limitations apparent from the source summary include absence of peer review (this work is a preprint) and lack of detailed methods and quantitative results in the summary text. The source did not report in vivo data, clinical dosing guidance, or safety data for doxycycline in UM patients; such translational steps would be required before clinical application.
The authors declared funding from The New York Eye and Ear Infirmary Foundation and reported no competing interests. The manuscript is posted as a bioRxiv preprint and has not been certified by peer review.
Overall, the work described in the source positions doxycycline as a candidate metabolic modulator that reduces UM‑associated growth, angiogenesis, and oxidative phosphorylation markers in a human ocular organoid model of BAP1 repression, supporting further investigation in preclinical and ultimately clinical settings.